4.5 Article

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi-sample genomic data

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae)

Yuichi Koshiishi et al.

Summary: The emu is a novel and useful breed of poultry, but their genetic improvement has been hindered by recent domestication and complex reproductive systems. This study isolated over 25,000 microsatellite regions, developed 49 SSR markers, and identified high levels of polymorphism in Japanese farmed emus. Additionally, parentage tests using these markers displayed a high success rate in identifying offspring-parent relationships.
Article Biochemistry & Molecular Biology

Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

Pengcheng Wang et al.

Summary: This study analyzed genomic data of three isolated populations of Brown eared pheasant in China, showing low genome-wide diversity and declining effective population size. The comparison with a closely related species revealed detrimental genetic consequences in the Brown eared pheasant genomes, indicating a potential risk of deleterious mutations in wild populations undergoing long-term decline. This comprehensive conservation genomic analysis could help improve conservation planning for threatened species and promote population recovery.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Agriculture, Dairy & Animal Science

Comparison of kinship estimates in Santa Ine circumflex accent s sheep using microsatellite and genome-wide SNP markers

Alzira Regina Silva de Deus et al.

Summary: The use of suitable molecular markers is crucial in preventing the loss of important traits in the Santa Ines breed of meat sheep in Brazil. By comparing the efficiency of microsatellite markers to a genome-wide SNP array, it was found that panels with less than 15 markers had lower efficiency, with most individuals being either unrelated or half siblings.

SMALL RUMINANT RESEARCH (2021)

Editorial Material Biochemistry & Molecular Biology

Confidently identifying the correct K value using the Delta K method: When does K=2?

Catherine I. Cullingham et al.

MOLECULAR ECOLOGY (2020)

Article Biochemical Research Methods

Myriads: P-value-based multiple testing correction

Antonio Carvajal-Rodriguez

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Genetics and the conservation of natural populations: allozymes to genomes

Fred W. Allendorf

MOLECULAR ECOLOGY (2017)

Review Plant Sciences

THE REPORT OF MY DEATH WAS AN EXAGGERATION: A REVIEW FOR RESEARCHERS USING MICROSATELLITES IN THE 21ST CENTURY

Richar D. G. J. Hodel et al.

APPLICATIONS IN PLANT SCIENCES (2016)

Article Biochemical Research Methods

The MaSuRCA genome assembler

Aleksey V. Zimin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

lobSTR: A short tandem repeat profiler for personal genomes

Melissa Gymrek et al.

GENOME RESEARCH (2012)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing

Jawad Abdelkrim et al.

BIOTECHNIQUES (2009)

Article Evolutionary Biology

Effects of Microsatellite Null Alleles on Assignment Testing

Jens Carlsson

JOURNAL OF HEREDITY (2008)

Review Biotechnology & Applied Microbiology

Mining microsatellites in eukaryotic genomes

Prakash C. Sharma et al.

TRENDS IN BIOTECHNOLOGY (2007)

Article Biochemistry & Molecular Biology

Microsatellite null alleles and estimation of population differentiation

Marie-Pierre Chapuis et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research

R Peakall et al.

MOLECULAR ECOLOGY NOTES (2006)

Article Ecology

Microsatellite null alleles in parentage analysis

EE Dakin et al.

HEREDITY (2004)